Tag Archives: animals

#437608 Video Friday: Agility Robotics Raises ...

Video Friday is your weekly selection of awesome robotics videos, collected by your Automaton bloggers. We’ll also be posting a weekly calendar of upcoming robotics events for the next few months; here’s what we have so far (send us your events!):

IROS 2020 – October 25-29, 2020 – [Online]
ROS World 2020 – November 12, 2020 – [Online]
CYBATHLON 2020 – November 13-14, 2020 – [Online]
ICSR 2020 – November 14-16, 2020 – Golden, Colo., USA
Let us know if you have suggestions for next week, and enjoy today’s videos.

Digit is now in full commercial production and we’re excited to announce a $20M funding rounding round co-led by DCVC and Playground Global!

Digits for everyone!

[ Agility Robotics ]

A flexible rover that has both ability to travel long distances and rappel down hard-to-reach areas of scientific interest has undergone a field test in the Mojave Desert in California to showcase its versatility. Composed of two Axel robots, DuAxel is designed to explore crater walls, pits, scarps, vents and other extreme terrain on the moon, Mars and beyond.

This technology demonstration developed at NASA’s Jet Propulsion Laboratory in Southern California showcases the robot’s ability to split in two and send one of its halves — a two-wheeled Axle robot — over an otherwise inaccessible slope, using a tether as support and to supply power.

The rappelling Axel can then autonomously seek out areas to study, safely overcome slopes and rocky obstacles, and then return to dock with its other half before driving to another destination. Although the rover doesn’t yet have a mission, key technologies are being developed that might, one day, help us explore the rocky planets and moons throughout the solar system.

[ JPL ]

A rectangular robot as tiny as a few human hairs can travel throughout a colon by doing back flips, Purdue University engineers have demonstrated in live animal models. Why the back flips? Because the goal is to use these robots to transport drugs in humans, whose colons and other organs have rough terrain. Side flips work, too. Why a back-flipping robot to transport drugs? Getting a drug directly to its target site could remove side effects, such as hair loss or stomach bleeding, that the drug may otherwise cause by interacting with other organs along the way.

[ Purdue ]

This video shows the latest results in the whole-body locomotion control of the humanoid robot iCub achieved by the Dynamic Interaction Control line at IIT-Istituto Italiano di Tecnologia in Genova (Italy). In particular, the iCub now keeps the balance while walking and receiving pushes from an external user. The implemented control algorithms also ensure the robot to remain compliant during locomotion and human-robot interaction, a fundamental property to lower the possibility to harm humans that share the robot surrounding environment.

This is super impressive, considering that iCub was only able to crawl and was still tethered not too long ago. Also, it seems to be blinking properly now, so it doesn’t look like it’s always sleepy.

[ IIT ]

This video shows a set of new tests we performed on Bolt. We conducted tests on 5 different scenarios, 1) walking forward/backward 2) uneven surface 3) soft surface 4) push recovery 5) slippage recovery. Thanks to our feedback control based on Model Predictive Control, the robot can perform walking in the presence of all these uncertainties. We will open-source all the codes in a near future.

[ ODRI ]

The title of this video is “Can you throw your robot into a lake?” The title of this video should be, “Can you throw your robot into a lake and drive it out again?”

[ Norlab ]

AeroVironment Successfully Completes Sunglider Solar HAPS Stratospheric Test Flight, Surpassing 60,000 Feet Altitude and Demonstrating Broadband Mobile Connectivity.

[ AeroVironment ]

We present CoVR, a novel robotic interface providing strong kinesthetic feedback (100 N) in a room-scale VR arena. It consists of a physical column mounted on a 2D Cartesian ceiling robot (XY displacements) with the capacity of (1) resisting to body-scaled users actions such as pushing or leaning; (2) acting on the users by pulling or transporting them as well as (3) carrying multiple potentially heavy objects (up to 80kg) that users can freely manipulate or make interact with each other.

[ DeepAI ]

In a new video, personnel from Swiss energy supply company Kraftwerke Oberhasli AG (KWO) explain how they were able to keep employees out of harm’s way by using Flyability’s Elios 2 to collect visual data while building a new dam.

[ Flyability ]

Enjoy our Ascento robot fail compilation! With every failure we experience, we learn more and we can improve our robot for its next iteration, which will come soon… Stay tuned for more!

FYI posting a robot fails video will pretty much guarantee you a spot in Video Friday!

[ Ascento ]

Humans are remarkably good at using chopsticks. The Guinness World Record witnessed a person using chopsticks to pick up 65 M&Ms in just a minute. We aim to collect demonstrations from humans and to teach robot to use chopsticks.

[ UW Personal Robotics Lab ]

A surprising amount of personality from these Yaskawa assembly robots.

[ Yaskawa ]

This paper presents the system design, modeling, and control of the Aerial Robotic Chain Manipulator. This new robot design offers the potential to exert strong forces and moments to the environment, carry and lift significant payloads, and simultaneously navigate through narrow corridors. The presented experimental studies include a valve rotation task, a pick-and-release task, and the verification of load oscillation suppression to demonstrate the stability and performance of the system.

[ ARL ]

Whether animals or plants, whether in the water, on land or in the air, nature provides the model for many technical innovations and inventions. This is summed up in the term bionics, which is a combination of the words ‘biology‘ and ‘electronics’. At Festo, learning from nature has a long history, as our Bionic Learning Network is based on using nature as the source for future technologies like robots, assistance systems or drive solutions.

[ Festo ]

Dogs! Selfies! Thousands of LEGO bricks! This video has it all.

[ LEGO ]

An IROS workshop talk on “Cassie and Mini Cheetah Autonomy” by Maani Ghaffari and Jessy Grizzle from the University of Michigan.

[ Michigan Robotics ]

David Schaefer’s Cozmo robots are back with this mind-blowing dance-off!

What you just saw represents hundreds of hours of work, David tells us: “I wrote over 10,000 lines of code to create the dance performance as I had to translate the beats per minute of the song into motor rotations in order to get the right precision needed to make the moves look sharp. The most challenging move was the SpongeBob SquareDance as any misstep would send the Cozmos crashing into each other. LOL! Fortunately for me, Cozmo robots are pretty resilient.”

[ Life with Cozmo ]

Thanks David!

This week’s GRASP on Robotics seminar is by Sangbae Kim from MIT, on “Robots with Physical Intelligence.”

While industrial robots are effective in repetitive, precise kinematic tasks in factories, the design and control of these robots are not suited for physically interactive performance that humans do easily. These tasks require ‘physical intelligence’ through complex dynamic interactions with environments whereas conventional robots are designed primarily for position control. In order to develop a robot with ‘physical intelligence’, we first need a new type of machines that allow dynamic interactions. This talk will discuss how the new design paradigm allows dynamic interactive tasks. As an embodiment of such a robot design paradigm, the latest version of the MIT Cheetah robots and force-feedback teleoperation arms will be presented.

[ GRASP ]

This week’s CMU Ri Seminar is by Kevin Lynch from Northwestern, on “Robotics and Biosystems.”

Research at the Center for Robotics and Biosystems at Northwestern University encompasses bio-inspiration, neuromechanics, human-machine systems, and swarm robotics, among other topics. In this talk I will give an overview of some of our recent work on in-hand manipulation, robot locomotion on yielding ground, and human-robot systems.

[ CMU RI ] Continue reading

Posted in Human Robots

#437571 Video Friday: Snugglebot Is What We All ...

Video Friday is your weekly selection of awesome robotics videos, collected by your Automaton bloggers. We’ll also be posting a weekly calendar of upcoming robotics events for the next few months; here's what we have so far (send us your events!):

IROS 2020 – October 25-25, 2020 – [Online]
Robotica 2020 – November 10-14, 2020 – [Online]
ROS World 2020 – November 12, 2020 – [Online]
CYBATHLON 2020 – November 13-14, 2020 – [Online]
ICSR 2020 – November 14-16, 2020 – Golden, Colo., USA
Bay Area Robotics Symposium – November 20, 2020 – [Online]
Let us know if you have suggestions for next week, and enjoy today's videos.

Snugglebot is what we all need right now.

[ Snugglebot ]

In his video message on his prayer intention for November, Pope Francis emphasizes that progress in robotics and artificial intelligence (AI) be oriented “towards respecting the dignity of the person and of Creation”.

[ Vatican News ]

KaPOW!

Apparently it's supposed to do that—the disruptor flies off backwards to reduce recoil on the robot, and has its own parachute to keep it from going too far.

[ Ghost Robotics ]

Animals have many muscles, receptors, and neurons which compose feedback loops. In this study, we designed artificial muscles, receptors, and neurons without any microprocessors, or software-based controllers. We imitate the reflexive rule observed in walking experiments of cats, as a result, the Pneumatic Brainless Robot II emerged running motion (a leg trajectory and a gait pattern) through the interaction between the body, the ground, and the artificial reflexes. We envision that the simple reflex circuit we discovered will be a candidate for a minimal model for describing the principles of animal locomotion.

Find the paper, “Brainless Running: A Quasi-quadruped Robot with Decentralized Spinal Reflexes by Solely Mechanical Devices,” on IROS On-Demand.

[ IROS ]

Thanks Yoichi!

I have no idea what these guys are saying, but they're talking about robots that serve chocolate!

The world of experience of the Zotter Schokoladen Manufaktur of managing director Josef Zotter counts more than 270,000 visitors annually. Since March 2019, this world of chocolate in Bergl near Riegersburg in Austria has been enriched by a new attraction: the world's first chocolate and praline robot from KUKA delights young and old alike and serves up chocolate and pralines to guests according to their personal taste.

[ Zotter ]

This paper proposes a systematic solution that uses an unmanned aerial vehicle (UAV) to aggressively and safely track an agile target. The solution properly handles the challenging situations where the intent of the target and the dense environments are unknown to the UAV. The proposed solution is integrated into an onboard quadrotor system. We fully test the system in challenging real-world tracking missions. Moreover, benchmark comparisons validate that the proposed method surpasses the cutting-edge methods on time efficiency and tracking effectiveness.

[ FAST Lab ]

Southwest Research Institute developed a cable management system for collaborative robotics, or “cobots.” Dress packs used on cobots can create problems when cables are too tight (e-stops) or loose (tangling). SwRI developed ADDRESS, or the Adaptive DRESing System, to provide smarter cobot dress packs that address e-stops and tangling.

[ SWRI ]

A quick demonstration of the acoustic contact sensor in the RBO Hand 2. An embedded microphone records the sound inside of the pneumatic finger. Depending on which part of the finger makes contact, the sound is a little bit different. We create a sensor that recognizes these small changes and predicts the contact location from the sound. The visualization on the left shows the recorded sound (top) and which of the nine contact classes the sensor is currently predicting (bottom).

[ TU Berlin ]

The MAVLab won the prize for the “most innovative design” in the IMAV 2018 indoor competition, in which drones had to fly through windows, gates, and follow a predetermined flight path. The prize was awarded for the demonstration of a fully autonomous version of the “DelFly Nimble”, a tailless flapping wing drone.

In order to fly by itself, the DelFly Nimble was equipped with a single, small camera and a small processor allowing onboard vision processing and control. The jury of international experts in the field praised the agility and autonomous flight capabilities of the DelFly Nimble.

[ MAVLab ]

A reactive walking controller for the Open Dynamic Robot Initiative's skinny quadruped.

[ ODRI ]

Mobile service robots are already able to recognize people and objects while navigating autonomously through their operating environments. But what is the ideal position of the robot to interact with a user? To solve this problem, Fraunhofer IPA developed an approach that connects navigation, 3D environment modeling, and person detection to find the optimal goal pose for HRI.

[ Fraunhofer ]

Yaskawa has been in robotics for a very, very long time.

[ Yaskawa ]

Black in Robotics IROS launch event, featuring Carlotta Berry.

[ Black in Robotics ]

What is AI? I have no idea! But these folks have some opinions.

[ MIT ]

Aerial-based Observations of Volcanic Emissions (ABOVE) is an international collaborative project that is changing the way we sample volcanic gas emissions. Harnessing recent advances in drone technology, unoccupied aerial systems (UAS) in the ABOVE fleet are able to acquire aerial measurements of volcanic gases directly from within previously inaccessible volcanic plumes. In May 2019, a team of 30 researchers undertook an ambitious field deployment to two volcanoes – Tavurvur (Rabaul) and Manam in Papua New Guinea – both amongst the most prodigious emitters of sulphur dioxide on Earth, and yet lacking any measurements of how much carbon they emit to the atmosphere.

[ ABOVE ]

A talk from IHMC's Robert Griffin for ICCAS 2020, including a few updates on their Nadia humanoid.

[ IHMC ] Continue reading

Posted in Human Robots

#437477 If a Robot Is Conscious, Is It OK to ...

In the Star Trek: The Next Generation episode “The Measure of a Man,” Data, an android crew member of the Enterprise, is to be dismantled for research purposes unless Captain Picard can argue that Data deserves the same rights as a human being. Naturally the question arises: What is the basis upon which something has rights? What gives an entity moral standing?

The philosopher Peter Singer argues that creatures that can feel pain or suffer have a claim to moral standing. He argues that nonhuman animals have moral standing, since they can feel pain and suffer. Limiting it to people would be a form of speciesism, something akin to racism and sexism.

Without endorsing Singer’s line of reasoning, we might wonder if it can be extended further to an android robot like Data. It would require that Data can either feel pain or suffer. And how you answer that depends on how you understand consciousness and intelligence.

As real artificial intelligence technology advances toward Hollywood’s imagined versions, the question of moral standing grows more important. If AIs have moral standing, philosophers like me reason, it could follow that they have a right to life. That means you cannot simply dismantle them, and might also mean that people shouldn’t interfere with their pursuing their goals.

Two Flavors of Intelligence and a Test
IBM’s Deep Blue chess machine was successfully trained to beat grandmaster Gary Kasparov. But it could not do anything else. This computer had what’s called domain-specific intelligence.

On the other hand, there’s the kind of intelligence that allows for the ability to do a variety of things well. It is called domain-general intelligence. It’s what lets people cook, ski, and raise children—tasks that are related, but also very different.

Artificial general intelligence, AGI, is the term for machines that have domain-general intelligence. Arguably no machine has yet demonstrated that kind of intelligence. This summer, a startup called OpenAI released a new version of its Generative Pre-Training language model. GPT-3 is a natural language processing system, trained to read and write so that it can be easily understood by people.

It drew immediate notice, not just because of its impressive ability to mimic stylistic flourishes and put together plausible content, but also because of how far it had come from a previous version. Despite this impressive performance, GPT-3 doesn’t actually know anything beyond how to string words together in various ways. AGI remains quite far off.

Named after pioneering AI researcher Alan Turing, the Turing test helps determine when an AI is intelligent. Can a person conversing with a hidden AI tell whether it’s an AI or a human being? If he can’t, then for all practical purposes, the AI is intelligent. But this test says nothing about whether the AI might be conscious.

Two Kinds of Consciousness
There are two parts to consciousness. First, there’s the what-it’s-like-for-me aspect of an experience, the sensory part of consciousness. Philosophers call this phenomenal consciousness. It’s about how you experience a phenomenon, like smelling a rose or feeling pain.

In contrast, there’s also access consciousness. That’s the ability to report, reason, behave, and act in a coordinated and responsive manner to stimuli based on goals. For example, when I pass the soccer ball to my friend making a play on the goal, I am responding to visual stimuli, acting from prior training, and pursuing a goal determined by the rules of the game. I make the pass automatically, without conscious deliberation, in the flow of the game.

Blindsight nicely illustrates the difference between the two types of consciousness. Someone with this neurological condition might report, for example, that they cannot see anything in the left side of their visual field. But if asked to pick up a pen from an array of objects in the left side of their visual field, they can reliably do so. They cannot see the pen, yet they can pick it up when prompted—an example of access consciousness without phenomenal consciousness.

Data is an android. How do these distinctions play out with respect to him?

The Data Dilemma
The android Data demonstrates that he is self-aware in that he can monitor whether or not, for example, he is optimally charged or there is internal damage to his robotic arm.

Data is also intelligent in the general sense. He does a lot of distinct things at a high level of mastery. He can fly the Enterprise, take orders from Captain Picard and reason with him about the best path to take.

He can also play poker with his shipmates, cook, discuss topical issues with close friends, fight with enemies on alien planets, and engage in various forms of physical labor. Data has access consciousness. He would clearly pass the Turing test.

However, Data most likely lacks phenomenal consciousness—he does not, for example, delight in the scent of roses or experience pain. He embodies a supersized version of blindsight. He’s self-aware and has access consciousness—can grab the pen—but across all his senses he lacks phenomenal consciousness.

Now, if Data doesn’t feel pain, at least one of the reasons Singer offers for giving a creature moral standing is not fulfilled. But Data might fulfill the other condition of being able to suffer, even without feeling pain. Suffering might not require phenomenal consciousness the way pain essentially does.

For example, what if suffering were also defined as the idea of being thwarted from pursuing a just cause without causing harm to others? Suppose Data’s goal is to save his crewmate, but he can’t reach her because of damage to one of his limbs. Data’s reduction in functioning that keeps him from saving his crewmate is a kind of nonphenomenal suffering. He would have preferred to save the crewmate, and would be better off if he did.

In the episode, the question ends up resting not on whether Data is self-aware—that is not in doubt. Nor is it in question whether he is intelligent—he easily demonstrates that he is in the general sense. What is unclear is whether he is phenomenally conscious. Data is not dismantled because, in the end, his human judges cannot agree on the significance of consciousness for moral standing.

Should an AI Get Moral Standing?
Data is kind; he acts to support the well-being of his crewmates and those he encounters on alien planets. He obeys orders from people and appears unlikely to harm them, and he seems to protect his own existence. For these reasons he appears peaceful and easier to accept into the realm of things that have moral standing.

But what about Skynet in the Terminator movies? Or the worries recently expressed by Elon Musk about AI being more dangerous than nukes, and by Stephen Hawking on AI ending humankind?

Human beings don’t lose their claim to moral standing just because they act against the interests of another person. In the same way, you can’t automatically say that just because an AI acts against the interests of humanity or another AI it doesn’t have moral standing. You might be justified in fighting back against an AI like Skynet, but that does not take away its moral standing. If moral standing is given in virtue of the capacity to nonphenomenally suffer, then Skynet and Data both get it even if only Data wants to help human beings.

There are no artificial general intelligence machines yet. But now is the time to consider what it would take to grant them moral standing. How humanity chooses to answer the question of moral standing for nonbiological creatures will have big implications for how we deal with future AIs—whether kind and helpful like Data, or set on destruction, like Skynet.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Image Credit: Ico Maker / Shutterstock.com Continue reading

Posted in Human Robots

#437466 How Future AI Could Recognize a Kangaroo ...

AI is continuously taking on new challenges, from detecting deepfakes (which, incidentally, are also made using AI) to winning at poker to giving synthetic biology experiments a boost. These impressive feats result partly from the huge datasets the systems are trained on. That training is costly and time-consuming, and it yields AIs that can really only do one thing well.

For example, to train an AI to differentiate between a picture of a dog and one of a cat, it’s fed thousands—if not millions—of labeled images of dogs and cats. A child, on the other hand, can see a dog or cat just once or twice and remember which is which. How can we make AIs learn more like children do?

A team at the University of Waterloo in Ontario has an answer: change the way AIs are trained.

Here’s the thing about the datasets normally used to train AI—besides being huge, they’re highly specific. A picture of a dog can only be a picture of a dog, right? But what about a really small dog with a long-ish tail? That sort of dog, while still being a dog, looks more like a cat than, say, a fully-grown Golden Retriever.

It’s this concept that the Waterloo team’s methodology is based on. They described their work in a paper published on the pre-print (or non-peer-reviewed) server arXiv last month. Teaching an AI system to identify a new class of objects using just one example is what they call “one-shot learning.” But they take it a step further, focusing on “less than one shot learning,” or LO-shot learning for short.

LO-shot learning consists of a system learning to classify various categories based on a number of examples that’s smaller than the number of categories. That’s not the most straightforward concept to wrap your head around, so let’s go back to the dogs and cats example. Say you want to teach an AI to identify dogs, cats, and kangaroos. How could that possibly be done without several clear examples of each animal?

The key, the Waterloo team says, is in what they call soft labels. Unlike hard labels, which label a data point as belonging to one specific class, soft labels tease out the relationship or degree of similarity between that data point and multiple classes. In the case of an AI trained on only dogs and cats, a third class of objects, say, kangaroos, might be described as 60 percent like a dog and 40 percent like a cat (I know—kangaroos probably aren’t the best animal to have thrown in as a third category).

“Soft labels can be used to represent training sets using fewer prototypes than there are classes, achieving large increases in sample efficiency over regular (hard-label) prototypes,” the paper says. Translation? Tell an AI a kangaroo is some fraction cat and some fraction dog—both of which it’s seen and knows well—and it’ll be able to identify a kangaroo without ever having seen one.

If the soft labels are nuanced enough, you could theoretically teach an AI to identify a large number of categories based on a much smaller number of training examples.

The paper’s authors use a simple machine learning algorithm called k-nearest neighbors (kNN) to explore this idea more in depth. The algorithm operates under the assumption that similar things are most likely to exist near each other; if you go to a dog park, there will be lots of dogs but no cats or kangaroos. Go to the Australian grasslands and there’ll be kangaroos but no cats or dogs. And so on.

To train a kNN algorithm to differentiate between categories, you choose specific features to represent each category (i.e. for animals you could use weight or size as a feature). With one feature on the x-axis and the other on the y-axis, the algorithm creates a graph where data points that are similar to each other are clustered near each other. A line down the center divides the categories, and it’s pretty straightforward for the algorithm to discern which side of the line new data points should fall on.

The Waterloo team kept it simple and used plots of color on a 2D graph. Using the colors and their locations on the graphs, the team created synthetic data sets and accompanying soft labels. One of the more simplistic graphs is pictured below, along with soft labels in the form of pie charts.

Image Credit: Ilia Sucholutsky & Matthias Schonlau
When the team had the algorithm plot the boundary lines of the different colors based on these soft labels, it was able to split the plot up into more colors than the number of data points it was given in the soft labels.

While the results are encouraging, the team acknowledges that they’re just the first step, and there’s much more exploration of this concept yet to be done. The kNN algorithm is one of the least complex models out there; what might happen when LO-shot learning is applied to a far more complex algorithm? Also, to apply it, you still need to distill a larger dataset down into soft labels.

One idea the team is already working on is having other algorithms generate the soft labels for the algorithm that’s going to be trained using LO-shot; manually designing soft labels won’t always be as easy as splitting up some pie charts into different colors.

LO-shot’s potential for reducing the amount of training data needed to yield working AI systems is promising. Besides reducing the cost and the time required to train new models, the method could also make AI more accessible to industries, companies, or individuals who don’t have access to large datasets—an important step for democratization of AI.

Image Credit: pen_ash from Pixabay Continue reading

Posted in Human Robots

#437171 Scientists Tap the World’s Most ...

In The Hitchhiker’s Guide to the Galaxy by Douglas Adams, the haughty supercomputer Deep Thought is asked whether it can find the answer to the ultimate question concerning life, the universe, and everything. It replies that, yes, it can do it, but it’s tricky and it’ll have to think about it. When asked how long it will take it replies, “Seven-and-a-half million years. I told you I’d have to think about it.”

Real-life supercomputers are being asked somewhat less expansive questions but tricky ones nonetheless: how to tackle the Covid-19 pandemic. They’re being used in many facets of responding to the disease, including to predict the spread of the virus, to optimize contact tracing, to allocate resources and provide decisions for physicians, to design vaccines and rapid testing tools, and to understand sneezes. And the answers are needed in a rather shorter time frame than Deep Thought was proposing.

The largest number of Covid-19 supercomputing projects involves designing drugs. It’s likely to take several effective drugs to treat the disease. Supercomputers allow researchers to take a rational approach and aim to selectively muzzle proteins that SARS-CoV-2, the virus that causes Covid-19, needs for its life cycle.

The viral genome encodes proteins needed by the virus to infect humans and to replicate. Among these are the infamous spike protein that sniffs out and penetrates its human cellular target, but there are also enzymes and molecular machines that the virus forces its human subjects to produce for it. Finding drugs that can bind to these proteins and stop them from working is a logical way to go.

The Summit supercomputer at Oak Ridge National Laboratory has a peak performance of 200,000 trillion calculations per second—equivalent to about a million laptops. Image credit: Oak Ridge National Laboratory, U.S. Dept. of Energy, CC BY

I am a molecular biophysicist. My lab, at the Center for Molecular Biophysics at the University of Tennessee and Oak Ridge National Laboratory, uses a supercomputer to discover drugs. We build three-dimensional virtual models of biological molecules like the proteins used by cells and viruses, and simulate how various chemical compounds interact with those proteins. We test thousands of compounds to find the ones that “dock” with a target protein. Those compounds that fit, lock-and-key style, with the protein are potential therapies.

The top-ranked candidates are then tested experimentally to see if they indeed do bind to their targets and, in the case of Covid-19, stop the virus from infecting human cells. The compounds are first tested in cells, then animals, and finally humans. Computational drug discovery with high-performance computing has been important in finding antiviral drugs in the past, such as the anti-HIV drugs that revolutionized AIDS treatment in the 1990s.

World’s Most Powerful Computer
Since the 1990s the power of supercomputers has increased by a factor of a million or so. Summit at Oak Ridge National Laboratory is presently the world’s most powerful supercomputer, and has the combined power of roughly a million laptops. A laptop today has roughly the same power as a supercomputer had 20-30 years ago.

However, in order to gin up speed, supercomputer architectures have become more complicated. They used to consist of single, very powerful chips on which programs would simply run faster. Now they consist of thousands of processors performing massively parallel processing in which many calculations, such as testing the potential of drugs to dock with a pathogen or cell’s proteins, are performed at the same time. Persuading those processors to work together harmoniously is a pain in the neck but means we can quickly try out a lot of chemicals virtually.

Further, researchers use supercomputers to figure out by simulation the different shapes formed by the target binding sites and then virtually dock compounds to each shape. In my lab, that procedure has produced experimentally validated hits—chemicals that work—for each of 16 protein targets that physician-scientists and biochemists have discovered over the past few years. These targets were selected because finding compounds that dock with them could result in drugs for treating different diseases, including chronic kidney disease, prostate cancer, osteoporosis, diabetes, thrombosis and bacterial infections.

Scientists are using supercomputers to find ways to disable the various proteins—including the infamous spike protein (green protrusions)—produced by SARS-CoV-2, the virus responsible for Covid-19. Image credit: Thomas Splettstoesser scistyle.com, CC BY-ND

Billions of Possibilities
So which chemicals are being tested for Covid-19? A first approach is trying out drugs that already exist for other indications and that we have a pretty good idea are reasonably safe. That’s called “repurposing,” and if it works, regulatory approval will be quick.

But repurposing isn’t necessarily being done in the most rational way. One idea researchers are considering is that drugs that work against protein targets of some other virus, such as the flu, hepatitis or Ebola, will automatically work against Covid-19, even when the SARS-CoV-2 protein targets don’t have the same shape.

Our own work has now expanded to about 10 targets on SARS-CoV-2, and we’re also looking at human protein targets for disrupting the virus’s attack on human cells. Top-ranked compounds from our calculations are being tested experimentally for activity against the live virus. Several of these have already been found to be active.The best approach is to check if repurposed compounds will actually bind to their intended target. To that end, my lab published a preliminary report of a supercomputer-driven docking study of a repurposing compound database in mid-February. The study ranked 8,000 compounds in order of how well they bind to the viral spike protein. This paper triggered the establishment of a high-performance computing consortium against our viral enemy, announced by President Trump in March. Several of our top-ranked compounds are now in clinical trials.

Also, we and others are venturing out into the wild world of new drug discovery for Covid-19—looking for compounds that have never been tried as drugs before. Databases of billions of these compounds exist, all of which could probably be synthesized in principle but most of which have never been made. Billion-compound docking is a tailor-made task for massively parallel supercomputing.

Dawn of the Exascale Era
Work will be helped by the arrival of the next big machine at Oak Ridge, called Frontier, planned for next year. Frontier should be about 10 times more powerful than Summit. Frontier will herald the “exascale” supercomputing era, meaning machines capable of 1,000,000,000,000,000,000 calculations per second.

Although some fear supercomputers will take over the world, for the time being, at least, they are humanity’s servants, which means that they do what we tell them to. Different scientists have different ideas about how to calculate which drugs work best—some prefer artificial intelligence, for example—so there’s quite a lot of arguing going on.

Hopefully, scientists armed with the most powerful computers in the world will, sooner rather than later, find the drugs needed to tackle Covid-19. If they do, then their answers will be of more immediate benefit, if less philosophically tantalizing, than the answer to the ultimate question provided by Deep Thought, which was, maddeningly, simply 42.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Image credit: NIH/NIAID Continue reading

Posted in Human Robots